Cell Biology Python Packages

cellpose

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

deepcell

Deep Learning Library for Single Cell Analysis

cellshape

3D shape analysis using deep learning

deepcell-cpu

Deep Learning Library for Single Cell Analysis

deepliif

Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24, MICCAI'26]

epitools

Quantifying 2D cell shape and epithelial tissue dynamics

cellpose-mcp

MCP tools for Cellpose and napari integration

actk

Automated Cell Toolkit

u-segment3d

Generate consensus 3D cells segmentations by combining 2D cell segmentations from any combination of xy, xz, yz views, compatible with outputs of any 2D segmentation method.

cello-classify

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

cellpyability

Software for the automated analysis of in cellulo high-throughput drug screening

cellpose-vollseg

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

biosimulations-bigg

Command-line program and scheduled GitHub action for publishing the BiGG model repository to BioSimulations

biosimulators-rbapy

RBApy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

deepcelltl

Deep Learning Library for Single Cell Analysis

cellgeometry

A web-based application for Cell Shape Analysis.

spheroidpy

Python Package for the Analysis of Spheroid Microcopy Data

u-unwrap3d

Transform 3D cell surfaces into different representations including topographic maps, 3D spheres, and 2D images for doing optimized quantification, data analysis and machine learning.

cellseg

Deep Learning Based Cell Segmentation

pyvertexmodel

3D vertex model allowing scutoids

optiflow

Reconstruction of flows from kymographs with optimal transport

cellsepi

A modular platform for end-to-end batch cell segmentation and quantification for microscopy images.

cytounet

Deep Learning Based Cell Segmentation

fluospotter

Fluospotter is an end-to-end pipeline designed for nuclei segmentation and puncta detection in fluorescence microscopy images.